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EMBL-PKU / BASALT

MIT License
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Error when running with test dataset：ModuleNotFoundError: No module named 'torch' #33

Open 1023011930 opened 1 month ago

1023011930 commented 1 month ago

nohup bash basalt.sh nohup.txt Basalt_log.txt basalt.txt

I used tencent cloud‘s basalt_env.yml

git clone https://github.com/EMBL-PKU/BASALT.git cd BASALT conda env create -n BASALT --file basalt_env.yml

mamba install pytorch torchvision torchaudio -c pytorch

如果遇到错误，请从腾讯云（https://share.weiyun.com/xXdRiDkl）下载basalt_env.yml并创建conda环境：

conda env create -n BASALT --file basalt_env.yml

安装的同时下载训练好的模型

https://share.weiyun.com/r33c2gqa

给权限

chmod -R 777 /home/XX/mambaforge/envs/BASALT/bin/* mv BASALT.zip ~/.cache cd ~/.cache unzip BASALT.zip BASALT -h

Bug： 4300 sequences 4300 >= 500 bp 4400 sequences 4400 >= 500 bp 4500 sequences 4500 >= 500 bp 4600 sequences 4600 >= 500 bp 4700 sequences 4700 >= 500 bp 4800 sequences 4800 >= 500 bp Parsing kmer 1_assembly.fa Reading basic information Processing Coverage_matrix_for_binning_1_assembly.fa.txt ['1_assembly.fa.kmer.txt'] mkdir: 无法创建目录"BestBinset_outlier_test": 文件已存在 Traceback (most recent call last): File "/home/zhongpei/mambaforge/envs/BASALT/bin/ensemble.py", line 10, in import torch ModuleNotFoundError: No module named 'torch' Predicting potential outliers Traceback (most recent call last): File "/home/zhongpei/mambaforge/envs/BASALT/bin/BASALT", line 141, in BASALT_main_c(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software) File "/home/zhongpei/mambaforge/envs/BASALT/bin/BASALT_main_c.py", line 441, in BASALT_main_c outlier_remover_main('BestBinset', coverage_matrix_list, datasets, assembly_mo_list, pwd, num_threads) File "/home/zhongpei/mambaforge/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 452, in outlier_remover_main A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, num_threads, nx) File "/home/zhongpei/mambaforge/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 145, in outlier_predictor for line in open('Predicted_potential_outlier.txt','r'): FileNotFoundError: [Errno 2] No such file or directory: 'Predicted_potential_outlier.txt'

1023011930 commented 1 month ago

I would appreciate a reply from you guys!

EMBL-PKU commented 1 month ago

Hi, I guess it is a problem of environment. You may need to re-install BASALT to solve this issue. Are you from China? If so, 可以加我的微信，yukechris，我看看问题

1023011930 commented 1 month ago

Here's how I solved it mamba install pytorch torchvision torchaudio -c pytorch pip install torch torchvision mamba install -c conda-forge tensorboardx